Interesting questions all!
I am using an external cooling system for the enlarger head ((there was a url link here which no longer exists)). I purchased the head used, and when it came to me one of the foam vibration-damping mounts for the internal cooling fan was broken. So when I turned on the fan, I could feel the head vibrating when I placed a finger one of the extremities of the enlarger head. I do not know how much of this vibration was due to the fan and how much was due to the broken fan mount. So I just dealt with it by building my own cooling system. I would suggest that any vibration that your finger could feel or any vibration that would disturb a glass of water resting on the head is enough to effect print sharpness, but you'd need to test your own equipment. Can you make a print with the fan turned on and the same print with the fan turned off?
I use a laser alignment system to align my enlarger, and because I use a glass negative carrier, the laser reflects from the negative carrier without any special attachments. My procedure is to load the negative carrier, remove the lensboard, align the easel to the negative carrier (I use a homemade version of the Ease-align system to adjust the easel rather than adjusting the negative carrier), then replace the lensboard and align the lensboard to the easel (by securing a small mirror to the lens threads and bouncing the laser beam from that and adjusting the Bes-Align adjustable lensboard). With this system, every time I load a new negative into the negative carrier I can check and adjust the system alignment. It takes 2 or 3 extra minutes each time and is worth it as far as I'm concerned. Especially because I find that the system is often out of alignment after removing the negative carrier, reloading it, and replacing it in the enlarger.
In his printing workshop John Wimberley recommends the following test for enlarging flare: Expose a whole sheet of paper to a Zone V density (test to determine what exposure this is). Leave the paper in the easel and hold a dodging card about 12" above the paper so that it will cover half of the paper when the enlarger light is turned back on. Place a small opaque object like a coin on the shaded half of the paper. Expose the paper, with the opaque object in place and half of the paper shielded by your dodging card, to light from the enlarger for four times your normal print exposure time. Process the paper normally. If you can see where the opaque object was, then you have enlarging flare. ic-racer, I think your test might also be valid. Flashing the paper to Zone V puts it on the steepest part of its HD curve before you do your enlarging flare test, and thus makes it the most sensitive to additional scattered light. Using a multiple of four times your normal exposure tests under worse case conditions like a negative that needs lots of burning, etc.